69 lines
1.7 KiB
Python
69 lines
1.7 KiB
Python
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#!/usr/bin/python
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#
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# Copyright 2018, Chanhee Park <parkchanhee@gmail.com> and Daehwan Kim <infphilo@gmail.com>
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#
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# This file is part of HISAT 2.
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#
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# HISAT 2 is free software: you can redistribute it and/or modify
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# it under the terms of the GNU General Public License as published by
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# the Free Software Foundation, either version 3 of the License, or
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# (at your option) any later version.
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#
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# HISAT 2 is distributed in the hope that it will be useful,
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# but WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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# GNU General Public License for more details.
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#
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# You should have received a copy of the GNU General Public License
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# along with HISAT 2. If not, see <http://www.gnu.org/licenses/>.
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#
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# ./setup.py build
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# ./setup.py install
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#
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import ht2py
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# Path to index
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ht2_index = '../../evaluation/indexes/HISAT2_22/22_rep'
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# Get default options
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ht2_options = ht2py.get_options()
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print ht2_options
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ht2_options['gVerbose'] = 1
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ht2_options['startVerbose'] = 1
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# or
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ht2_options = {}
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handle = ht2py.init(ht2_index, ht2_options)
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print ht2py.index_getrefnamebyid(handle, 0)
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#print ht2py.index_getrefnamebyid(handle, 0, 1, 3, 5, 7, 9)
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# outofindex
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#print ht2py.index_getrefnamebyid(handle, 1)
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#print ht2py.index_getrefnamebyid(handle, -1)
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refnames = ht2py.index_getrefnames(handle)
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#for name in refnames:
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# print name
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# repeat expansion
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positions = ht2py.repeat_expand(handle, 'rep100-300', 8308, 100)
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for pos in positions:
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chr_id = pos[0]
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direction = pos[1]
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chr_pos = pos[2]
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chr_dir = '+'
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if direction == 1:
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chr_dir = '-'
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print refnames[chr_id].split()[0] + ":" + str(chr_pos) + ':' + chr_dir
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# close handle
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ht2py.close(handle)
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